title: U2OS, nRIP-LC3B

city: Suwon-si

first: Ho Chul

last: Kang

state: Gyeonggi-do

address: World cup-ro, Yeongtong-gu

department: Physiology

country: South Korea

institute: Ajou university school of medicine

description: protocol: nRIP-seq

data_processing:
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: U2OS cells were maintained in DMEM supplemented with 10% fetal boviin serum(FBS). Cell were cultured at 37 in 5% CO2

extract_protocol:
RNA was prepared using Magna Nuclear RIP™ (Native) Nuclear RNA-Binding Protein Immunoprecipitation Kit(Sigma) following manufacture protocol.
RNA libralies for RIP-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit following manufacture protocol.

value: Osteosarcoma

tag: rip antibody

value: LC3B(Cell signaling, 3868S)


title: RING1BmAID-TAF1dTAG-T7-UNT-rep1

status: Public on May 29 2024

type: SRA

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description:
Untreated control for TAF1-T7 ChIP-seq in RING1BminiAID;TAF1-T7-dTAG mESCs
RING1BmAID_TAF1dTAG_T7_UNT_mm10.normalisedSpikeInInput.MERGED.MACS2.bw

library_source: genomic

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+hg19) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
Sequencing datasets were calibrated to the spike-in human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools.
Assembly: mm10; hg19
Supplementary files format and content: Genome coverage tracks were generated using the pileup function from MACS2.
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
5 x 10^7 ESCs were fixed with 1% formaldehyde (methanol-free, Thermo Fisher Scientific) for 10 min at 25⁰C. Fixation was quenched using glycine added to 125 mM. Cells were then pelleted at 1000xg for 5 min and washed with PBS. Cross-linked ESCs were mixed with 1 x 10^6 cross-linked HEK 293T/T7-SCC1 cells (1% formaldehyde for 10 min; a gift from Martin Houlard, Nasmyth lab). Chromatin was prepared by incubation in 1 ml FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x PIC, 10 mM NaF) on ice for 10 min. Chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode) at 4⁰C for 23 cycles (30s on/off) to an average size of 0.5 kb. The sonicated material was pelleted at 20,000xg for 20 min, and the supernatant taken as sonicated chromatin. 300 μg chromatin was used per IP. Chromatin was diluted to 1 ml total volume per IP in FA-lysis buffer. An additional volume of diluted chromatin was taken to use as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in 1x TE buffer at 4⁰C for 1 hr. Chromatin was pre-cleared with agarose beads (40 μl slurry beads per ChIP) at 4⁰C for 1 - 2 hr. The input sample was taken from the pre-cleared chromatin, and the remainder was immunoprecipitated overnight at 4⁰C with 5μl T7 (Cell Signalling, D9E1X). Antibody-bound chromatin was precipitated for 3 hr at 4⁰C using 40 μl slurry of blocked Protein A agarose beads. Washes were carried out for 5 min each at 4⁰C, using ice-cold FA-lysis buffer, FA-lysis buffer with 500 mM NaCl, 1x DOC buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 1 mM EDTA , 0.5% NP-40, 0.5% Na-deoxycholate), and 2 washes with TE buffer. DNA was eluted in elution buffer (1% SDS and 0.1 M NaHCO3). Cross-links were reversed for ChIPs and inputs at 65⁰C overnight with 200 mM NaCl and 2 μl RNase A (Sigma). Samples were then incubated with 20 μg Proteinase K for 1 hr at 45⁰C. DNA for ChIPs and inputs was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). Purified DNA was analysed using ChIP-qPCR.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate on Illumina NextSeq 500 platform.

treatment_protocol: Cell lines expressing were treated with 100 nM dTAG-13 (Tocris Bioscience) or 500 µM IAA (Sigma) for 4 hours to induce protein depletion.

tag: cell line

tag: cell type

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in.

tag: treatment

value: untreated

tag: treatment time

tag: replicate

tag: spike-in reference

value: Homo sapiens

tag: spike-in cell_line

value: HEK293T; Scc1-T7

tag: antibody

value: anti-T7 (Cell Signalling D9E1X)


title: RBG26414_Plate_4_KO

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

library_source: transcriptomic single cell

data_processing:
RNA-seq reads were aligned to mm10 + ERCC92 using GSNAP (version 2018-03-25) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.9.1) with the parameter (-s no).
Assembly: GRCm38.81
Supplementary files format and content: HTSeq counts text file with raw counts and htseq metrics
Supplementary files format and content: Anndata h5 file with filtered cells and genes and data transformations (in layers)

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Bone marrow cells were harvested from STAT5KO and WT control mice, single ESLAM HSCs was FACS sorted into 2.3ul 0.2% Triton-100 containg RNAse inhibitor
Tagmentation is carried out using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm.

tag: tissue

value: bone marrow

value: ESLAM

tag: genotype

value: KO


title: U2OS, nRIP-IgG

description: protocol: nRIP-seq

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens


title: RBG26405_Plate_3_KO


title: RBG26410_Plate_4_WT

value: WT


title: RBG26404_Plate_3_KO


title: Cells of NSCLC, patient 47

city: Suzhou

first: Junhong

last: Jiang

address: No.1 Songtao Street

country: China

institute: Dushu Lake Hospital Affiliated to Soochow University

data_processing:
Genomics Workbench v11.0.1
Assembly: hg18
Supplementary files format and content: tab-delimited text files include raw count for each Sample

source_name: lung

extract_protocol:
RNA extract Kits(Qiagen)
Pool libraries if necessary and load them onto the sequencing platform (e.g., Illumina NovaSeq). Perform high-throughput sequencing according to the manufacturer’s instructions.

tag: individual

value: patient 47

value: lung

value: Cells of NSCLC


title: Cells of NSCLC, patient 46

value: patient 46


title: Cells of NSCLC, patient 45

value: patient 45


title: RBG26406_Plate_4_WT


title: RBG26407_Plate_4_WT


title: U2OS, Input-LC3B

description: protocol: nRIP-seq


title: Cells of NSCLC, patient 44

value: patient 44


title: U2OS, Input-IgG

description: protocol: nRIP-seq

value: Osteosarcoma


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6-, control - VDJ

city: Bethesda

first: Beatriz

last: León

state: Maryland

address: Building 10, Room 11N240A, 10 Center Drive

department: NIAID

country: USA

institute: NIH

description:
Mem_CD4_Tcells_CRTH2posCCR6neg_control_all_contig_annotations.csv
Mem_CD4_Tcells_CRTH2posCCR6neg_control_consensus.fasta

data_processing:
10x Genomics single cell mRNA, feature barcode, and VDJ libraries were sequenced on a NovaSeq 6000 S2 26x91 cycle run. Demultiplexing was performed using Cell Ranger mkfastq version 5.0.0. Cell Ranger count version 5.0.0 using the 10x reference GRCh38-2020-A using default parameters created count matrices for the mRNA and feature barcode data. A feature reference CSV file containing TotalSeq™-C Human Universal Cocktail, V1.0 antibody and UMI references alongside the 10 HTOs and UMI references for each sequenced sample. Seurat v4.1.3 was used to perform QC and analyze gene expression, ADT, and HTO data using the 10x filtered matrix. Additional filtering in Seurat was performed keeping cells with an nFeature_RNA count between 200 and 3000 and a mitochondrial percentage less than 15. HTO demux was used to demultiplex hashtags with a positive quantile of 0.99 to determine the HTO max id, negatives, and doublets. Filarial infected samples were integrated with their corresponding control cell subsets. The R package celldex v1.8.0 Database of Immune Cell Expression (DICE) fine markers annotated cells using SingleR v2.0.0. Differential expression testing was performed using MAST with the latent variable set as “nCount_RNA” and minimum percent of cells set as 20%. Repertoire data was analyzed using scRepertoire v1.8.0.
Assembly: GRCh38-2020-A
Supplementary files format and content: 10x Genomics Cell Ranger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: 10x Genomics Cell Ranger VDJ Output Files: contig_annotations.csv, barcodes.tsv.gz, consensus.fasta

source_name: PBMCs

extract_protocol:
Multiomic single cell immune profiling was performed in three subsets of memory CD4+ T cells enriched among filarial-infected patients. Briefly, from PBMCs of ten filarial-infected patients (four HDM-Filarial+ and six HDM+Filarial+) and ten healthy donor volunteers (five HDM+Filarial- and five HDM-Filarial-), three subsets of effector memory (CCR7-CD45RO+) CD4+ T cells were sorted out, including CD4+ T cells expressing CCR4+CCR6+CRTH2- (subset 1), CCR4+CCR6-CRTH2+ (subset 2), and CCR4+CCR6+CRTH2+ (subset 3).
Approximately 1 x 104 sorted cells of each subset from all patients were hash-tagged separately with TotalSeq™-C anti-human hashtag (Biolegend). After that, each patient’s cells subsets were pooled together accordingly for a total of 10,000 cells per sample, generating a total of 6 samples. Approximately 1 x 104 multiplexed cells (a thousand cells per patient for each sorted subset) were stained with TotalSeq™-C Human Universal Cocktail (Biolegend) and then loaded into the Chromium Next GEM Chip G (10x Genomics) respectively. In total, 18 libraries were made in accordance with the Chromium Single Cell V(D)J Reagent Kits User Guide (v1.1) with Feature Barcoding technology, including 6 GEX libraries, 6 VDJ-enriched libraries and 6 Cell Surface Protein libraries.

value: PBMCs

tag: library type

value: VDJ


title: RBG26400_Plate_3_KO


title: RBG26411_Plate_4_WT


title: RBG26401_Plate_3_KO


title: Cells of NSCLC, patient 43

value: patient 43


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6-, control - GEX/HTO

description:
Mem_CD4_Tcells_CRTH2posCCR6neg_control_barcodes.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6neg_control_features.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6neg_control_matrix.mtx.gz
Mem_CD4_Tcells_CRTH2posCCR6neg_control_feature_reference.csv

value: GEX/HTO


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6-, control - ADT

value: ADT


title: Cells of NSCLC, patient 42

value: patient 42


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6+, control - VDJ

description:
Mem_CD4_Tcells_CRTH2posCCR6pos_control_all_contig_annotations.csv
Mem_CD4_Tcells_CRTH2posCCR6pos_control_consensus.fasta


title: RBG26402_Plate_3_KO

value: bone marrow


title: d32_DC2_3

city: SAINT LOUIS

first: Suin

last: Jo

state: MO

address: 4939 Childrens PI

department: Division of Biology & Biomedical Sciences

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed using Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR ver-sion 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Assembly: Mouse Ensembl GRCm38.76 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with merged differential expression results

source_name: Spleen

growth_protocol: cDC1 or cDC2 (100,000 cells per sample) were sort-purified from the spleens of WT, Irf8 +32-/-, or Zeb2 -165(d1+2+3).

extract_protocol:
RNA was isolated from approximately 100,000 splenic DCs using NucleoSpin RNA XS Kit (Macherey-Nagel).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Libraries were prepared with 10 ng of total RNA using a Bioanalyzer RIN score greater than 8.0. ds-cDNA preparation was done by the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol and sequenced on an Illumina NovaSeq X Plus using pared end reads extending 150 bases.

treatment_protocol: The cells were collected into 100 μL MACS buffer containing 40 U of Protector RNase inhibitor (Roche) to prevent RNA degradation

value: Spleen

value: Sort-purified (untreated)


title: RBG26403_Plate_3_KO

value: ESLAM

value: KO


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6+, control - ADT

description:
Mem_CD4_Tcells_CRTH2posCCR6pos_control_barcodes.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6pos_control_features.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6pos_control_matrix.mtx.gz
Mem_CD4_Tcells_CRTH2posCCR6pos_control_feature_reference.csv


title: Cells of NSCLC, patient 38

value: patient 38

value: lung


title: d32_DC2_2


title: Tri_DC1_3


title: RBG26397_Plate_3_WT

value: WT


title: RBG26396_Plate_3_WT


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6+, control - GEX/HTO


title: Tri_DC1_2


title: Cells of NSCLC, patient 36

value: patient 36

value: Cells of NSCLC


title: RING1BmAID-TAF1dTAG-T7-Input-UNT-rep1

description: Input for untreated control for TAF1-T7 ChIP-seq in RING1BminiAID;TAF1-T7-dTAG mESCs

value: Mouse embryonic stem cells with human T7-Scc1 HEK293T cells spike-in.

value: untreated

value: Homo sapiens

value: HEK293T; Scc1-T7


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2-CCR6+, control - VDJ

description:
Mem_CD4_Tcells_CRTH2negCCR6pos_control_all_contig_annotations.csv
Mem_CD4_Tcells_CRTH2negCCR6pos_control_consensus.fasta

value: PBMCs

value: VDJ


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2-CCR6+, control - ADT

description:
Mem_CD4_Tcells_CRTH2negCCR6pos_control_barcodes.tsv.gz
Mem_CD4_Tcells_CRTH2negCCR6pos_control_features.tsv.gz
Mem_CD4_Tcells_CRTH2negCCR6pos_control_matrix.mtx.gz
Mem_CD4_Tcells_CRTH2negCCR6pos_control_feature_reference.csv

value: ADT


title: WT_DC2_3


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2-CCR6+, control - GEX/HTO

value: GEX/HTO


title: WT_DC2_2

value: Spleen


title: Cells of NSCLC, patient 34

value: patient 34


title: Gclc KO 3 Batch 1-2

city: Rochester

first: Isaac

middle: Spencer

last: Harris

state: New York

address: 601 Elmwood Ave

department: Department of Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Demultiplexing software version: bcl2fastq2 v2.2.
Differential expression and GSEA analyses were performed as previously described1,2.
References:
1. Frazee, A. C. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol 33, 243-246 (2015). https://doi.org/10.1038/nbt.3172
2. Korotkevich, G. et al. Fast gene set enrichment analysis. bioRxiv, 060012 (2021). https://doi.org/10.1101/060012
Assembly: Mus musculus
Supplementary files format and content: Excel file with normalized counts.

source_name: Liver

growth_protocol: Gclc f/f and Gclc f/f Rosa26-CreERT2 mice were treated with tamoxifen (i.p., 150 mg/kg, 5 days). After 14 days, mice were sacrifice and the liver was harvested.

extract_protocol:
RNA extracted using Invitrogen PureLink RNA Mini Kit
RNA libraries for RNA-seq were prepared using Kapa mRNA Directional Library Preparation following manufacturers protocols.

value: Liver

value: Gclc KO


title: WT_DC1_3

value: Sort-purified (untreated)


title: Cells of NSCLC, patient 35

value: patient 35

value: lung


title: RBG26398_Plate_3_WT

value: bone marrow

value: ESLAM

value: WT


title: Cells of NSCLC, patient 32

value: patient 32

value: Cells of NSCLC


title: WT_DC1_2


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6-, filarial infected - ADT

description:
Mem_CD4_Tcells_CRTH2posCCR6neg_filarial_barcodes.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6neg_filarial_features.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6neg_filarial_matrix.mtx.gz
Mem_CD4_Tcells_CRTH2posCCR6neg_filarial_feature_reference.csv


title: RBG26395_Plate_3_WT


title: RBG26399_Plate_3_WT


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6-, filarial infected - VDJ

description:
Mem_CD4_Tcells_CRTH2posCCR6neg_filarial_all_contig_annotations.csv
Mem_CD4_Tcells_CRTH2posCCR6neg_filarial_consensus.fasta


title: Cells of NSCLC, patient 30

value: patient 30


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6-, filarial infected - GEX/HTO

value: PBMCs


title: RBG26394_Plate_3_WT


title: Bile duct cells for RRV infected mouse 7 days post sample 2

type: RNA

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

description: R 0_7 4

hyb_protocol: Samples were hybridized to the GeneChip Mouse Exon 1.0 ST Array platform (Affymetrix, Santa Clara, CA) which contains 1.2 million probe sets per chip. An initial genome-wide analysis was performed using GeneSpring GX (Agilent)

scan_protocol: Scanned with GCS 3000 HR. AGCC 6.1, DEC 2.0 used for image processing.

data_processing:
Data was processed with GeneSpring
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps
Normalized gene level expression values from GeneSpring
differentially_expressed_probesets.txt: An initial genome-wide analysis was performed using GeneSpring GX (Agilent), identifying genes from RRV challenged animals that were over- or under-expressed 1.5-fold as compared to control samples using one-way analysis of variance (ANOVA) with post-hoc t-testing. A false discovery rate (FDR) of 5% was used. Significance was set at p<0.05.

label: biotin

source_name: Cholangiocytes from Bile Ducts

label_protocol: RNA quality and quantity was assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Pico Chip (Agilent Technologies, Palo Alto, CA) (13). In this study, RNA quality was determined by several factors previously shown to be predictive of intact RNA (14): an RNA integrity number (RIN) ≥ 6.5 and 28S peak area under the curve (AUC) > 18S peak AUC.

growth_protocol: 7 day old BALB/c mice

extract_protocol: RNA was extracted and purified from these cholangiocytes using the RNeasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.

treatment_protocol: 3 pups injected with saline and 3 pups injected with RRV at birth

tag: developmental stage

value: 7 days

tag: strain

value: BALB/c

value: pooled LCM bile ducts

value: RRV infected mouse 7 days post sample


title: Cells of NSCLC, patient 29

value: patient 29


title: Bile duct cells for RRV infected mouse 7 days post sample 3

description: R 0_7 6


title: Bile duct cells for RRV infected mouse 7 days post sample 1

description: R 0_7 3


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6+, filarial infected - VDJ

description:
Mem_CD4_Tcells_CRTH2posCCR6pos_filarial_all_contig_annotations.csv
Mem_CD4_Tcells_CRTH2posCCR6pos_filarial_consensus.fasta

value: VDJ


title: RBG26389_Plate_3_KO

value: KO


title: RBG26393_Plate_3_KO


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6+, filarial infected - ADT

description:
Mem_CD4_Tcells_CRTH2posCCR6pos_filarial_barcodes.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6pos_filarial_features.tsv.gz
Mem_CD4_Tcells_CRTH2posCCR6pos_filarial_matrix.mtx.gz
Mem_CD4_Tcells_CRTH2posCCR6pos_filarial_feature_reference.csv

value: ADT


title: Cells of NSCLC, patient 28

value: patient 28


title: RBG26388_Plate_3_KO


title: Cells of NSCLC, patient 27

value: patient 27

value: lung


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2+CCR6+, filarial infected - GEX/HTO

value: GEX/HTO


title: Bile duct cells for Saline injected mouse 7 days post sample 3

description: S 0_7 10

value: Saline injected mouse 7 days post


title: RBG26392_Plate_3_KO

value: bone marrow

value: ESLAM


title: Cells of NSCLC, patient 31

value: patient 31

value: Cells of NSCLC


title: Bile duct cells for Saline injected mouse 7 days post sample 2

description: S 0_7 5

value: 7 days


title: Cells of NSCLC, patient 40

value: patient 40


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2-CCR6+, filarial infected - VDJ

description:
Mem_CD4_Tcells_CRTH2negCCR6pos_filarial_all_contig_annotations.csv
Mem_CD4_Tcells_CRTH2negCCR6pos_filarial_consensus.fasta

value: PBMCs


title: RBG26391_Plate_3_KO


title: Cells of NSCLC, patient 26

value: patient 26


title: Bile duct cells for Saline injected mouse 7 days post sample 1

description: S 0_7 2

value: BALB/c

value: pooled LCM bile ducts


title: RBG26390_Plate_3_KO

value: KO


title: RBG26385_Plate_3_WT

value: WT


title: Cells of NSCLC, patient 25

value: patient 25


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2-CCR6+, filarial infected - ADT

description:
Mem_CD4_Tcells_CRTH2negCCR6pos_filarial_barcodes.tsv.gz
Mem_CD4_Tcells_CRTH2negCCR6pos_filarial_features.tsv.gz
Mem_CD4_Tcells_CRTH2negCCR6pos_filarial_matrix.mtx.gz
Mem_CD4_Tcells_CRTH2negCCR6pos_filarial_feature_reference.csv

value: ADT


title: Cells of NSCLC, patient 24

value: patient 24

value: lung


title: Cells of NSCLC, patient 23

value: patient 23


title: RBG26387_Plate_3_WT

value: bone marrow


title: 4-RVz16 CD8

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Cell Ranger  v3.1 software was used to perform demultiplexing of cellular transcript data, and mapping and annotation of UMIs and transcripts for downstream data analysis.
Assembly: Mmul10 from Ensembl release 100
Supplementary files format and content: H5 archive or cellbarcoded transcript counts

organism: Macaca mulatta

source_name: Lymph Node

extract_protocol:
Cryopreserved LN samples from 5 A*01+ animals at D42 p.i. were thawed and stained with the following antibodies: anti-CD8-FITC (clone RPA-T8, BD Biosciences), anti-CD4-BV650 (clone OKT4, Biolegend), anti-Gag-PE (CM9 tetramer, NIH Tetramer Facility at Emory University, anti-CD95-PE/Cy7 (clone DX2, BD Biosciences), anti-CD28-APC (clone CD28.2, BD Biosciences), anti-CD3-APC/Cy7 (clone SP34-2, BD Biosciences). A minimum of 10,000 SIV-specific CD8 from each animal was sorted using a FACS Aria II system and loaded onto 10X Chromium Controller.
Single cells were partitioned into droplets (Gel Beads in Emulsion: GEMs) using Chromium NextGEM Single Cell 5’ Library & Gel Bead kits on the 10X Chromium Controller. The resulting cDNA was amplified and libraries were prepared for transcriptomic analysis according to manufacturer instructions. Gene expression libraries were sequenced as paired-end 26x91 reads on an Illumina NovaSeq6000 targeting a depth of 50,000 reads per cell.

value: Lymph Node

tag: subject


title: 3-RNy16 CD8


title: 5-RYm17 CD8


title: Jurkat T cells Matr3 KO 1

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

data_processing:
To avoid reads with artificial bias, we removed the following type of reads:1) Reads with ≥ 10% unidentified nucleotides (N);2) Reads pair with aligned to the adapter;3) Reads with > 50% bases having phred quality < 5;
Clean reads were aligned to the NT database using Blast mem v 2.2.26.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie2 and clean reads were aligned to the reference genome using Bowtie2. Then valid paired reads were obtained by filtering with HICPro v2.11.1. The iterative correction (ICE) method was applied to normalize interaction matrices to eliminate the bias of raw matrices.
Observed interaction matrix was an interaction matrix after the statistics of the finally valid contacts according to a certain resolution. Building and normalizing observed interaction matrix with pastis.
Assembly: hg38
Supplementary files format and content: each processed data file for each Sample

source_name: Jurkat T cells

growth_protocol: Jurkat T cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Briefly, after the completion crosslinking and lysis, chromatin was digested with 200U DPN II restriction enzyme (Qiagen) at 37 °C.
DNA fragments were purified and dissolved in water. Unligated ends were then removed. Purified DNA was fragmented to a size of 350-500 bp, and DNA ends were then repaired. DNA fragments labeled by biotin were finally separated on Dynabeads® M-280 Streptavidin (Life Technologies).

treatment_protocol: Knock out MATR3 by crisp cas9 or not

value: Jurkat T cells

value: T cell

value: Matr3 knock out


title: Cells of NSCLC, patient 22

value: patient 22

value: Cells of NSCLC


title: Cells of NSCLC, patient 21

value: patient 21


title: RBG26386_Plate_3_WT

value: ESLAM


title: 2-RHm17 CD8


title: RUNX1R320_RNA_3

city: La Jolla

first: Dong-Er

last: Zhang

state: California

address: 3855 Health Sciences Dr

department: Pathology

institute: University of California, San Diego

data_processing:
RPKM values derived from Salmon1.2.1 using Tx2Gene.v31
Normalized counts were derived from HISAT2 aligned reads followed by featureCounts and normalization with DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file DESeq2 normalized counts
Supplementary files format and content: tab-delimited text file Salmon derived RPKM

growth_protocol: K562 human leukemia cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin Streptomycin antibiotics in humidified atmosphere 5% CO2 at 37 C

extract_protocol:
Cell suspensions were spun down at 500 x g and RNA was extracted using TRIzol reagent and manufacturer's protocol
NEBNext Ultra™ II RNA Library Prep Kit for Illumina

value: leukemia

value: RUNX1 R320*


title: RBG26382_Plate_3_WT

value: WT


title: Cells of NSCLC, patient 37

value: patient 37


title: Cells of NSCLC, patient 20

value: patient 20


title: Cells of NSCLC, patient 19

value: patient 19


title: RUNX1R320_RNA_1


title: L3 animals with dat-1 NanoDam and FOS-1::GFP, replicate 3

city: Stanford

first: Callista

last: Yee

address: 327 Campus Drive, Shen lab, Bass Biology 329

institute: Stanford University/HHMI

description:
MinION Mk1C
dat-1_NanoDam_FOS-1_rep3
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep3.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep3.peaks.gff

data_processing:
Nanopore sequences were basecalled and demultiplexed using guppy 3.6 onboard a MinION Mk1C device, only base calling reads with a Q score higher than 8.
Fastq files were combined together using the UNIX command 'cat' and mapped to the ce10 genome using minimap2 with the options '-ax map-ont' to output .sam files.
SAM files were sorted and converted to bam using samtools.
Sorted .bam files and a file mapping all GATC sequences in C. elegans were fed into damidseq_pipeline (Marshall and Brand, 2015) to obtain bedgraph files.
Bedgraphs were analyzed for peaks using find_peaks (Owen Marshall).
Assembly: ce10
Supplementary files format and content: .bedgraphs represent the comparisons between the NanoDam alone control vs. NanoDam binding to a transcription factor
Supplementary files format and content: .gff files represent the called peaks after analysis of the .bedgraph files

organism: Caenorhabditis elegans

source_name: Dopaminergic Neurons

growth_protocol: Animals grown for 3 generations on Dam- bacteria (E. coli ER2925 from NEB) were bleach synchronized and L1s were grown at 25C until the L3 stage (24h after putting L1s on food). Approximately 5000 synchronized worms were harvested, washed with M9, then snap frozen in liquid nitrogen and stored at -80C.

extract_protocol:
gDNA was harvested using a Qiagen DNeasy Tissue and Blood kit (#69504) with no deviations from standard protocols.
DamID amplicons were obtained as previously described (Gomez-Saldivar et al., 2021) using 4 initial PCR cycles followed by 19 additional cycles. DamID amplicons were directly barcoded through blunt end ligation and sequenced using Oxford Nanopore library reagents (LSK-109, NBD-104, NBD-114)

value: Dopaminergic Neurons

tag: sample type

value: Specific expression of Dam in target tissue


title: RUNX1R320_RNA_2


title: RBG26383_Plate_3_WT

value: bone marrow


title: Memory CD4+ T cells CD45RO+CCR7lowCCR4+CRTH2-CCR6+, filarial infected - GEX/HTO

value: PBMCs

value: GEX/HTO


title: Cells of NSCLC, patient 18

value: patient 18

value: lung


title: RBG26380_Plate_3_KO

value: KO


title: 1-RFl17 CD8

value: Lymph Node


title: RBG26381_Plate_3_KO


title: Cells of NSCLC, patient 17

value: patient 17

value: Cells of NSCLC


title: RBG26378_Plate_3_KO

value: ESLAM


title: L3 animals with dat-1 NanoDam and FOS-1::GFP, replicate 1

description:
MinION Mk1C
dat-1_NanoDam_FOS-1_rep1
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep1.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep1.peaks.gff


title: Jurkat T cells 1

value: Jurkat T cells

value: T cell


title: L3 animals with dat-1 NanoDam and EGL-43::GFP, replicate 3

description:
MinION Mk1C
dat-1_NanoDam_EGL-43_rep3
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep3.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep3.peaks.gff


title: Cells of NSCLC, patient 16

value: patient 16


title: RBG26376_Plate_3_KO


title: RBG26384_Plate_3_WT

value: WT


title: L3 animals with dat-1_NanoDam control, replicate 3

description:
MinION Mk1C
dat-1_NanoDam_Alone_rep3
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep3.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep3.peaks.gff
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep3.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep3.peaks.gff


title: RUNX1R320_GRID_1

library_source: other

data_processing:
Reads were trimmed with Cutadapt v1.12 and aligned using BWA mem, custom scripts previously described in Li et al., 2017; Zhou et al., 2019 were used for downstream analysis in conjuction with the BEDtools software suite
Assembly: hg38
Supplementary files format and content: tab-delimited text file of GRID-seq detected RNA interactions with DNA regions
Library strategy: GRID-seq

molecule: other

extract_protocol:
Dual cross-linking (DSG 2 mM 45 mins room temperature; 3% formaldehyde 10 minutes room temperature) performed sequentially
Custom library prep (Li et al., 2017; Zhou et al., 2019)

value: leukemia

value: RUNX1 R320*


title: Cells of NSCLC, patient 15

value: patient 15


title: L3 animals with dat-1 NanoDam and EGL-43::GFP, replicate 1

description:
MinION Mk1C
dat-1_NanoDam_EGL-43_rep1
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep1.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep1.peaks.gff

value: Dopaminergic Neurons

value: Specific expression of Dam in target tissue


title: WT_RNA_1


title: RBG26379_Plate_3_KO

value: bone marrow


title: L3 animals with dat-1 NanoDam and FOS-1::GFP, replicate 2

description:
MinION Mk1C
dat-1_NanoDam_FOS-1_rep2
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep2.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep2.peaks.gff


title: RUNX1R320_GRID_2


title: Cells of NSCLC, patient 14

value: patient 14


title: Cells of NSCLC, patient 13

value: patient 13

value: lung


title: WT_GRID_1


title: L3 animals with dat-1_NanoDam control, replicate 2

description:
MinION Mk1C
dat-1_NanoDam_Alone_rep2
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep2.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep2.peaks.gff
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep2.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep2.peaks.gff


title: RBG26377_Plate_3_KO

value: KO


title: WT_RNA_3


title: WT_GRID_2


title: RBG26374_Plate_3_WT


title: WT_RNA_2


title: L3 animals with dat-1_NanoDam control, replicate 1

description:
MinION Mk1C
dat-1_NanoDam_Alone_rep1
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep1.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep1.peaks.gff
Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep1.bedgraph
Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep1.peaks.gff


title: RBG26372_Plate_3_WT


title: Cells of NSCLC, patient 11

value: patient 11


title: L3 animals with dat-1 NanoDam and EGL-43::GFP, replicate 2

description:
MinION Mk1C
dat-1_NanoDam_EGL-43_rep2
Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep2.bedgraph
Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep2.peaks.gff


title: Adjacent non-cancerous cells of NSCLC, patient 47

value: patient 47

value: Adjacent non-cancerous cells of NSCLC


title: RBG26373_Plate_3_WT

value: ESLAM


title: RUNX1R320_1

data_processing:
Reads were trimmed with Cutadapt v1.12 and aligned to hg38 using BWA mem. Duplicates were removed with PICARD and genes annotated Gencode v31 annotation.
CPM normalization was used to generate the included coverage (bigWig) flies
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
1% formaldehyde fixation for 10 minutes at room temperature with occasional inversion. DNA was sonicated with Covaris M220.
NEB Next Ultra II DNA Library Prep Kit

tag: chip antibody

value: RUNX1 Abcam 23980


title: SIA replicate-id 242 [SIAr242]

city: New Haven

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

institute: Yale University

data_processing:
Trimming TruSeq adapters using BBMap version 38.90, command bbduk, options ktrim=r k=23 mink=11 hdist=1 tpe tbo
Alignment using STAR version 2.7.7a, option --outFilterMatchNminOverLread 0.3
Deduplication based on Tecan SoLo Ovation UMIs, using umi-tools version 1.1.4, commands extract and dedup
Counting reads per gene using Subread version 2.0.3, command featureCounts
Assembly: Wormbase annotation WS289

source_name: FACS isolated SIA neurons

growth_protocol: Worms were grown on 8P nutrient agar 150 mm plates seeded with E. coli strain NA22

extract_protocol:
RNA was isolated using chloroform extraction
Libraries were prepared using Tecan SoLo Ovation RNAseq library

treatment_protocol: Sorting protocol: Fluorescence Activated Cell Sorting (FACS) was performed on a BD FACSAria™ III equipped with a 70-micron diameter nozzle. Cells were sorted into Trizol reagent LS

value: FACS isolated SIA neurons

value: SIA


title: Adjacent non-cancerous cells of NSCLC, patient 46

value: patient 46


title: SIA replicate-id 243 [SIAr243]


title: SIA replicate-id 241 [SIAr241]


title: RUNX1R320_Input

tag: cell line

value: leukemia

value: RUNX1 R320*

value: input


title: Adjacent non-cancerous cells of NSCLC, patient 45

value: patient 45

tag: cell type


title: SIA replicate-id 240 [SIAr240]


title: RBG26371_Plate_3_WT

value: bone marrow

value: WT


title: RBG26368_Plate_3_KO


title: Cells of NSCLC, patient 12

value: patient 12

value: Cells of NSCLC

tag: treatment


title: Adjacent non-cancerous cells of NSCLC, patient 44

value: patient 44

value: lung


title: Adjacent non-cancerous cells of NSCLC, patient 42

value: patient 42


title: RBG26369_Plate_3_KO

value: KO


title: WT_ChIP_1


title: RME replicate-id 251 [RMEr251]

source_name: FACS isolated RME neurons

value: FACS isolated RME neurons

value: RME


title: RBG26375_Plate_3_WT

value: ESLAM


title: RUNX1R320_2

value: RUNX1 Abcam 23980


title: RBG26367_Plate_3_KO


title: U2OS cells, shWSB2, TNF-α 2

city: shanghai

first: Yaning

last: Du

address: shanghai

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: U2OS cells were cultured in McCoy's 5a supplemented with 10% (v/v) fetal bovine serum and penicillin (50 U/ml) /streptomycin (50 µg/ml)  in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from cells with Trizol reagent (Invitrogen) according to the manufacturer’s instructions. 0.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina kits.

value: human osteosarcomacell

value: WSB2 knockdown

value: TNF-α

tag: time

value: 5 hours


title: RME replicate-id 249 [RMEr249]


title: Adjacent non-cancerous cells of NSCLC, patient 41

value: patient 41

value: Adjacent non-cancerous cells of NSCLC


title: RME replicate-id 250 [RMEr250]


title: Adjacent non-cancerous cells of NSCLC, patient 38

value: patient 38


title: RBG26370_Plate_3_WT

value: bone marrow

value: WT


title: WT_ChIP_2

value: leukemia


title: RBG26366_Plate_3_KO


title: U2OS cells, shWSB2, TNF-α 1


title: PVQ replicate-id 236 [PVQr236]

source_name: FACS isolated PVQ neurons

value: FACS isolated PVQ neurons

value: PVQ


title: RBG26365_Plate_3_KO

value: KO


title: PVQ replicate-id 235 [PVQr235]


title: Adjacent non-cancerous cells of NSCLC, patient 37

value: patient 37

value: lung


title: WT_ChIP_Input

value: input


title: RBG26364_Plate_3_KO

value: ESLAM


title: Adjacent non-cancerous cells of NSCLC, patient 36

value: patient 36


title: U2OS cells, shControl, TNF-α 1

value: human osteosarcomacell


title: RBG26363_Plate_3_WT


title: PVQ replicate-id 234 [PVQr234]


title: PVQ replicate-id 233 [PVQr233]


title: Adjacent non-cancerous cells of NSCLC, patient 35

value: patient 35


title: U2OS cells, shWSB2, normal 1

value: WSB2 knockdown


title: Adjacent non-cancerous cells of NSCLC, patient 34

value: patient 34


title: U2OS cells, shWSB2, normal 2


title: PVP replicate-id 5 [PVPr5]

source_name: FACS isolated PVP neurons

value: FACS isolated PVP neurons

value: PVP


title: Adjacent non-cancerous cells of NSCLC, patient 33

value: patient 33

value: Adjacent non-cancerous cells of NSCLC


title: RBG26361_Plate_3_WT

value: bone marrow

value: WT


title: RBG26362_Plate_3_WT


title: PVP replicate-id 4 [PVPr4]


title: Adjacent non-cancerous cells of NSCLC, patient 32

value: patient 32


title: U2OS cells, shControl, normal 2


title: U2OS cells, shControl, normal 1


title: PVP replicate-id 3 [PVPr3]


title: U2OS cells, shControl, TNF-α 2

value: TNF-α

value: 5 hours


title: RBG26360_Plate_3_WT


title: Adjacent non-cancerous cells of NSCLC, patient 31

value: patient 31

value: lung


title: GX109-T1c-5seq

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

institute: The University of Hong Kong

description: 10x Genomics

data_processing:
Sequence data was mapped to the human genome (GRCh38) using CellRanger DNA (version 2.2.0) for demultiplexing and estimating copy number on individual cells.
Assembly: GRCh38
Supplementary files format and content: GX109-T1c.count.txt: Tab-delimited text file
Supplementary files format and content: GX109-T1c.cell_info.txt: Tab-delimited text file

source_name: Human gastric cancer tissue

extract_protocol: Single cell encapsulation and cDNA libraries were prepared by Chromium™ Single Cell 5’ Reagent Kits and Chromium™ Single Cell A Chip Kit version 1. Cells in suspension are counted and loaded into individual wells of 10X Chromium Single Cell chip. Single cells are then encapsulated into Gel in-beads emulsions (GEM) by 10X Chromium Controller. Single Cell 5’ Reagent Kits is used to perform downstream steps, in brief as follows: reverse transcription is performed on GEMs, followed by cDNA clean up and amplification. The double-stranded cDNA will then go through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection per manufacturer’s protocol. Library size and concentration is determined by Qubit, quantitative PCR and Bioanalyzer assays. The libraries are denatured and diluted to optimal concentration. Illumina NovaSeq reagent kit is used for sequencing run at 150 bp for read 1 and read 2, each 10X sample index set comprises of 4 indexes. Sequencing was performed by Centre for PanorOmic Sciences, The University of Hong Kong using Novaseq 6000.

value: Human gastric cancer tissue


title: PVP replicate-id 2 [PVPr2]


title: Adjacent non-cancerous cells of NSCLC, patient 30

value: patient 30


title: 12-RSV-IgG

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

institute: The University of Edinburgh

description:
index 12 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz

data_processing:
cutadapt with parameters: --cores 15 --minimum-length=18 --adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC
Data was processed with our lab's CLEAR-CLIP pipeline https://github.com/sujaikumar/bucklab please refer to the GitHub page and our paper to learn further details of processing
Briefly, to detect miRNA-chimeric. The first part of the read was aligned to miRBase database was made with bowtie2. Then if the second part is longer than 18 nt, this fragment gets aligned to the human genome with bowtie2, the aligned part is extracted and this is then aligned with ShortStack in order to get clusters.
The clusters are then annotated with bedtools, looking for overlaps with each of the potential annotations available. Annotations were downloaded from Gencode v34 and regulatory regions were downloaded from Ensembl. Introns were defined with AGAT.
Assembly: GRCh38.primary_assembly.genome.fa from Gencode version 34
Supplementary files format and content: csv file with chromosome coordinates for binding sites for each miRNA, additional columns include expression levels in mock or RSV conditions, overlapping genome annotations are specified as individual columns with the gene name for that feature (CDS, rRNA, tRNA, promoter, etc)
Supplementary files format and content: the file also has information about the seed binding sites for miRNAs in each loci, as well as the actual miRNA and target sequence
Library strategy: CLEAR-CLIP

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using equal volume of Acid-phenol:chloroform (Ambion) followed by ethanol precipitation of the RNA
Libraries were generated using the Trilink CleanTag small RNA library kit according to manufacture's instructions, starting with the 5'adapter as the 3'adapter was ligated during the CLEAR-CLIP protocol

treatment_protocol: Cells were either Mock or RSV-infected (MOI 0.1) for 48h, then the cells were UV crosslinked at indicated doses, cells were lysed and RNase & DNase treated, AGO2-RNA complexes were immunoprecipitated using anti-AGO2 antibody, intermolecular ligation was used to generate chimeric sequences of miRNA-target RNA, a fluorescently labelled 3'sequencing adapter was ligated and fluorescent signal was used to purify AGO2-miRNA-target complexes from an SDS-PAGE, purified complexes were proteinase K treated to remove protein before RNA extraction

value: lung epithelial cells

value: RSV-infected, UV:200mJ/cm2

tag: molecular weight_of_purified_complexes

tag: ip antibody

value: Rat IgG2a kappa Isotype Control (eBR2a, Invitrogen, cat. 14-4321-82)


title: RBG26358_Plate_3_WT

value: ESLAM


title: HSN replicate-id 239 [HSNr239]

source_name: FACS isolated HSN neurons

value: FACS isolated HSN neurons

value: HSN


title: 09-mock

description:
index 9 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz

value: Mock-infected, UV:200mJ/cm2

value: AGO2 (clone 11A9, Merck, cat. MABE253)


title: Adjacent non-cancerous cells of NSCLC, patient 29

value: patient 29

value: Adjacent non-cancerous cells of NSCLC


title: RBG26357_Plate_3_KO

value: bone marrow

value: KO


title: Adjacent non-cancerous cells of NSCLC, patient 28

value: patient 28


title: 08-mock

description:
index 8 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz

value: WT


title: HSN replicate-id 238 [HSNr238]


title: RBG26356_Plate_3_KO


title: RBG26355_Plate_3_KO


title: HSN replicate-id 237 [HSNr237]


title: DVB replicate-id 267 [DVBr267]

source_name: FACS isolated DVB neurons

value: FACS isolated DVB neurons

value: DVB


title: Adjacent non-cancerous cells of NSCLC, patient 26

value: patient 26

value: lung


title: DVB replicate-id 266 [DVBr266]


title: RBG26354_Plate_3_KO


title: Adjacent non-cancerous cells of NSCLC, patient 25

value: patient 25


title: 05-RSV

description:
index 5 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz

value: lung epithelial cells

value: RSV-infected, UV:200mJ/cm2


title: RBG26359_Plate_3_WT

value: ESLAM


title: DVB replicate-id 265 [DVBr265]


title: 02-RSV

description:
index 2 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz


title: RBG26353_Plate_3_KO


title: 01-RSV

description:
index 1 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz


title: CEP replicate-id 281 [CEPr281]

source_name: FACS isolated CEP neurons

value: FACS isolated CEP neurons

value: CEP


title: Adjacent non-cancerous cells of NSCLC, patient 23

value: patient 23


title: 06_Mock (A549_CLEAR_200_UP)

description:
index 6 (TriLink), seq project 11804_Buck_Amy
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz

value: Mock-infected, UV:200mJ/cm2

value: AGO2 (clone 11A9, Merck, cat. MABE253)


title: Adjacent non-cancerous cells of NSCLC, patient 27

value: patient 27

value: Adjacent non-cancerous cells of NSCLC


title: CEP replicate-id 279 [CEPr279]


title: Adjacent non-cancerous cells of NSCLC, patient 24

value: patient 24


title: RBG26219_Plate_1_WT

source_name: bone marrow

value: bone marrow

value: WT


title: 04-RSV

description:
index 4 (TriLink), seq project 2019-09-sarah-clash
2022-11-08.RSV1245Mock689Igg.hsa-mature.human.18.mirnaclusters.stranded.samplecounts.annotated.targetseq.maturemirnaseq.all.GEO.csv.gz


title: Adjacent non-cancerous cells of NSCLC, patient 21

source_name: lung

value: patient 21


title: CEP replicate-id 278 [CEPr278]


title: A549_CLEAR_400_UP

description: index 5 (TriLink), seq project 11804_Buck_Amy

value: Mock-infected, UV:400mJ/cm2


title: CEP replicate-id 269 [CEPr269]


title: RBG26216_Plate_1_WT


title: Adjacent non-cancerous cells of NSCLC, patient 20

value: patient 20

value: lung


title: A549_CLEAR_400_DOWN

description: index 12 (TriLink), seq project 11804_Buck_Amy

value: lung epithelial cells


title: A549_CLEAR_200_DOWN

description: index 13 (TriLink), seq project 11804_Buck_Amy


title: Adjacent non-cancerous cells of NSCLC, patient 19

value: patient 19


title: A549_CLEAR_NCL_UP

description: index 7 (TriLink), seq project 11804_Buck_Amy

value: Mock-infected, UV:0mJ/cm2


title: RBG26217_Plate_1_WT

value: ESLAM


title: A549_CLEAR_NCL_ DOWN

description: index 14 (TriLink), seq project 11804_Buck_Amy


title: RBG26352_Plate_3_KO

value: KO


title: RBG26222_Plate_1_KO


title: Adult nosGAL4 WT #3

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: dm6
Supplementary files format and content: .csv, raw salmon gene counts

organism: Drosophila melanogaster

source_name: Ovary tissue

extract_protocol:
Ovaries were dissected into PBS and transferred to RNase free microcentrifuge tubes. PBS was removed and 100ul of Trizol was added and ovaries were flash frozen and stored at -80 C. Ovaries were then lysed in the microcentrifuge tube using a plastic disposable pestle. Trizol was added to 1 mL total volume while vigorously shaking the tubes and incubated for 5 min at RT. The samples were centrifuged for 20 min at >13,000 g at 4 C, and the supernatant was transferred to a fresh microcentrifuge tube. 500 ul of chloroform was added, and the samples were vigorously shaken and incubated for 5 minutes at RT. Samples were spun at max speed for 10 minutes at 4 C. The supernatant was transferred to a fresh microcentrifuge tube and ethanol precipitated. Sodium acetate was added, equaling 10% of the volume transferred and 2-2.5 volumes of 100% ethanol were added. The samples were shaken thoroughly and left to precipitate at -20 C overnight. The samples were centrifuged at max speed at 4 C for 15 min to pellet the RNA. The supernatant was discarded and 500 ul of 75% ethanol was added to wash the pellet. The samples were vortexed to dislodge the pellet to ensure thorough washing. The samples were spun at 4 C for 5 min and the supernatant was discarded. The pellets were dried for 10-20 min and then resuspended in 20-50ul of RNAse-free water and the absorbance at 260 was measured on a nanodrop to measure the concentration of each sample.
RNA libraries for RNA-seq were prepared using Netflex Rapid Directional RNAseq Kit (Perkin Elmer) following manufacturer's protocol.

value: Ovary tissue

tag: dissection

value: dissected 1-3 days post-eclosion

value: Adult


title: Adult nosGAL4 WT #2


title: Adjacent non-cancerous cells of NSCLC, patient 18

value: patient 18


title: RBG26218_Plate_1_WT

data_processing:
RNA-seq reads were aligned to mm10 + ERCC92 using GSNAP (version 2018-03-25) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.9.1) with the parameter (-s no).
Assembly: GRCm38.81
Supplementary files format and content: HTSeq counts text file with raw counts and htseq metrics
Supplementary files format and content: Anndata h5 file with filtered cells and genes and data transformations (in layers)

extract_protocol:
Bone marrow cells were harvested from STAT5KO and WT control mice, single ESLAM HSCs was FACS sorted into 2.3ul 0.2% Triton-100 containg RNAse inhibitor
Tagmentation is carried out using the Illumina Nextera XT DNA sample preparation kit. The protocol is based on the Tagmentation protocol from Fluidigm.


title: Adjacent non-cancerous cells of NSCLC, patient 22

data_processing:
Genomics Workbench v11.0.1
Assembly: hg18
Supplementary files format and content: tab-delimited text files include raw count for each Sample

extract_protocol:
RNA extract Kits(Qiagen)
Pool libraries if necessary and load them onto the sequencing platform (e.g., Illumina NovaSeq). Perform high-throughput sequencing according to the manufacturer’s instructions.

value: patient 22

value: Adjacent non-cancerous cells of NSCLC


title: Adult nosGAL4 WT #1


title: RBG26223_Plate_1_KO

value: bone marrow


title: RBG26220_Plate_1_KO


title: A549 Mock-infected, 48 hpi, polyphosphatase-treated, 3

description:
index 28, seq project 11540
102_Uninfected_48hpi

data_processing:
cutadapt with parameters: --cores 15 --max-n=0 --minimum-length=18 --maximum-length=100 --adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC
quickmirseq with parameters: REFINE_MISMATACH_READS=yes, SPECIES=human
then ran the following on mapped.csv file to subset columns of interest: zcat mapped.csv.gz | perl -plne ' s/\s+//g;s/,$//;' | awk -F"," 'NR==1 || ($2==0 && $6!="")' | cut -f1,10-16 -d"," | pigz -c > quickmirseq.mapped.mirna.filtered.GEO.csv.gz
Assembly: GRCh38.primary_assembly.genome.fa
Supplementary files format and content: csv file with unique reads, their counts across libraries and the miRNA they were assigned to by quickmirseq

extract_protocol:
RNA was extracted using miRNeasy kit (Qiagen), 1ug of extracted RNA was polyphosphatase-treated and 100ng were used as input for library preparation
Libraries were generated using the Trilink CleanTag small RNA library kit according to manufacture's instructions

treatment_protocol: Cells were either Mock or RSV-infected (MOI 0.1) and cells were harvested at different time points up to 96 h post infection (hpi)

value: WT

value: Mock infection, polyphosphatase-treated

value: 48 hpi


title: A549 RSV-infected, 48 hpi, polyphosphatase-treated, 3

description:
index 37, seq project 11540
111_RSV_48hpi

value: RSV infection, polyphosphatase-treated


title: Adjacent non-cancerous cells of NSCLC, patient 15

value: patient 15

value: lung


title: BEAF32-AB KO #2

value: BEAF 32-AB KO


title: bamGAL4-mediated stwl GKD #2

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: dm6
Supplementary files format and content: .csv, salmon gene counts

value: bamGAL4>stwl RNAi/TM6


title: Adjacent non-cancerous cells of NSCLC, patient 13

value: patient 13


title: RBG26221_Plate_1_KO

value: ESLAM

value: KO


title: BEAF32-AB KO #1

value: Ovary tissue

value: dissected 1-3 days post-eclosion


title: A549 RSV-infected, 48 hpi, polyphosphatase-treated, 2

description:
index 45, seq project 11540
83_RSV_48hpi

value: lung epithelial cells


title: RBG26214_Plate_1_WT


title: Adjacent non-cancerous cells of NSCLC, patient 14

value: patient 14


title: RBG26215_Plate_1_WT


title: A549 Mock-infected, 48 hpi, polyphosphatase-treated, 2

description:
index 36, seq project 11540
74_Uninfected_48hpi


title: bamGAL4-mediated stwl GKD #1

value: Adult


title: A549 RSV-infected, 48 hpi, polyphosphatase-treated, 1

description:
index 17, seq project 11540
55_RSV_48hpi


title: Adjacent non-cancerous cells of NSCLC, patient 12

value: patient 12

value: Adjacent non-cancerous cells of NSCLC


title: A549 Mock-infected, 48 hpi, polyphosphatase-treated, 1

description:
index 8, seq project 11540
46_Uninfected_48hpi

value: WT

value: Mock infection, polyphosphatase-treated


title: Adjacent non-cancerous cells of NSCLC, patient 17

value: patient 17


title: Adjacent non-cancerous cells of NSCLC, patient 11

value: patient 11


title: HEK293 Disome-seq [SM090Fd]

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

data_processing:
library strategy: ribosome profiling
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence by Cutadapt. These files are the raw data files uploaded on the GEO database.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
A custom python script is used to remove PCR duplicates by comparing the 7-nucleotide unique molecular identifiers (UMIs) in the libraries.
After trimming UMIs by Cutadapt, reads were aligned to human transcriptome by bowtie1 and mapped reads were processed by using custom python scripts.
Assembly: hg38
Supplementary files format and content: Custom ribosome occupancy files (pkl.gz extension)

source_name: T-REx 293

growth_protocol: DMEM media (high glucose) with 2 mM L-glutamine and 10% FBS

extract_protocol:
Lysates were clarified, treated with RNase I, and subjected to sucrose cushion to isolate ribosome footprints. RNA was then extracted using Trizol and footprints of the specified size were retained by gel purification.
RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Qiagen Fast-Select kit is used for removing rRNA during reverse transcription.

treatment_protocol: Cells were harvested by flash freezing and thawed in the presence of lysis buffer.

value: T-REx 293

value: Human embryonic kidney

tag: molecule type

value: disome footprints


title: nosGAL4-mediated stwl GKD #2

tag: tissue

value: nosGAL4;stwl RNAi/TM6


title: dsFragmentase_artificial_R_loop

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

data_processing:
bigWig
Supplementary files format and content: bigWig
Library strategy: ssDRIP-seq

organism: synthetic construct

source_name: artificial R-loop

extract_protocol: To prepare half R-loop substrates, RNA (5’-GGGAUGGUGCUGGACUCAUUCGGCAUCGGCGCUACAGAAGAUGCAGAACGCUUUGGUGACGUCGGGGCUGACACCCUGGGUCAUAUCGCAGAAGCUUGUGCCAAAGGCGAAGCUGAUAACGGUCGUAAAGGCCCGCUCAAUCUGCCAAAUCUGACCCGUCUGGGGCUGGCGAAAGCACACGAAGGUUCUACCGGUUUCAUUCC-3’) was produced by using in vitro transcription kit (New England Biolabs; M0658) and purified with phenol-chloroform method. In the following reverse transcription step, PCR templates was removed by gDNA digester (YEASEN; 11141ES10), followed by cDNA synthesis with primer (5’-ACGTGTCATGACTGACACTGGCAGTACGTAGCAGTGGTAGAACCTTCGTGTGC-3’) and paired DNA oligo (5’-TTCTACCACGGAACTGCTACGTACTGCCAGTGTCAGTCATGACACGT-3’). following the protocol (YEASEN; 11141ES10). The artificial R-loop was purified by 2 volumes of SPRIselect beads. 10 ng purified artificial R-loop was mixed with 20 U mung bean nuclease, S1 nuclease, dsDNase, dsDNA Fragmentase respectively, and incubated at 37°C for 10 min. The digested product was purified using 1.8 volumes of SPRIselect beads. Purified product was DRIPed and used for ssDNA library construction as described previously (ssDRIP-seq, Xu et al., 2017). The library was sequenced on an Illumina NovaSeq system.

value: artificial R-loop


title: bamGAL4 WT #1

tag: genotype


title: bamGAL4 WT #2


title: Uranus (iPSC line #2)

city: Hannover

first: Svenja

last: Gaedcke

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: 10x Genomics

data_processing:
The 10x Genomics CellRanger analysis pipeline set (v7.1.0) was used with default parameters. Briefly, BCL files were demultiplexed into FASTQ files by cellranger mkfastq using the respective sample sheet with utilized 10x barcodes. The cellranger count pipeline was used to align read data to the reference genome provided by 10x Genomics (Human reference dataset refdata-gex-GRCh38-2020-A), counting aligned reads per gene, and calculating clustering and summary statistics. Subsequently, outputs from cellranger count of all samples were aggregated, normalized to the same sequencing depth, and then the feature-barcode matrices were recomputed by cellranger aggr
Assembly: Human reference (GRCh38) datasets
Supplementary files format and content: tap separated  values and matrix files

source_name: iPSC line - LiPSC-GR1.1 (https://hpscreg.eu/cell-line/RUCDRi002-A)

extract_protocol:
freshly harvested iPSC-macrophages from the differentiation plate.
Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics). According to the protocol, a given excess of cells was loaded to the 10x controller in order to reach a target number of 4,000 cells per sample. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (ThermoFisher Scientific #Q32854).

value: iPSC-derived macrophages


title: Phoenix (iPSC line#3)

description: 10x Genomics

source_name: iPSC line -hHSC_Iso4_ADCF_SeViPS2 (https://hpscreg.eu/cell-line/MHHi001-A)


title: dsDNase_artificial_R_loop


title: nosGAL4-mediated stwl GKD #1

value: Ovary tissue


title: 293FT cell, lactate, Flag-IP, rep2

first: junyi

last: ju

address: 301 middle yanchang road

institute: Shanghai Tenth People’s Hospital

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <30 bp) and low quality reads using fastp (v0.20.0). Then FastQC was used to  perform quality control. Trimmed reads were aligned to the human reference genome hg19 using Bowtie2 (v2.2.6) and saved with format of bam by SAMtools (v1.10).
Peaks were called using MACS2(v2.2.7.1) with the parameters by default. FDR cut-off of 0.05 was used to determine significant peaks. ChIPseeker R package was invoked to annotate nearest genes and genomic features to peaks. Differentially peaks were identified by MAnorm2 with a cut-off value of log2|foldchange|>1 and p-value <0.05.
The clusterProfiler was used to perform functional enrichment analysis for the annotated significant peaks based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). HOMER(v4.11) was utilized to search for sequence motif among significant peaks. E value cutoff of 0.05 was used to select significantly enriched motifs.

source_name: HEK293FT cell

growth_protocol: Control group 293FT cells are cultured with glucose-free DMEM in 10cm dish for 24h

extract_protocol: Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Qsonica Q800R3 Sonicator.

treatment_protocol: Lactate group 293FT cells are cultured with glucose-free DMEM with 25mM lactate in 10mM dish for 24h

value: HEK293FT cell

value: human embryonic kidney cell

value: Flag

tag: chip target

value: clutured in glucose-free DMEM with exogenous 25mM lactate


title: 21s004532

city: Granada

first: Francisco

last: Hernandez-Torres

state: Granada

address: Avda. de la Investigación, 11

department: Dept. of Biochemistry, Molecular Biology III and Immunology

country: Spain

institute: Universidad de Granada

description:
DCM_19_miRNA
named_count_matrix_miR.xlsx

data_processing:
European version of the Galaxy platform (https://usegalaxy.eu/)
Reads were trimmed with the Trim Galore software (Galaxy Version 0.6.7+galaxy0)
Trimmed sequences reads were aligned to the built-in human reference genome Dec. 2013 (GRCh38/hg38) with the RNA STAR Gapped-read mapper (Galaxy Version 2.7.10b+galaxy3)
For gene expression analyses, bam files were downloaded from the Galaxy server and further analyzed with the different RStudio packages downloaded from the Bioconductor website (http://bioconductor. org).
Reads were assigned to genes by means of the “featureCounts” function of the “Rsubread” package, version 2.10.5. and annotation files human release 43 (GRCh38.p13) (https://www.gencodegenes.org/human/release_43.html) and Chromosomal coordinates of Homo sapiens microRNAs (https://www.mirbase.org/ftp/CURRENT/genomes/hsa.gff3) for mRNA and miRNA analysis respectively.
Assembly: hg38
Supplementary files format and content: execel file includes raw mRNA count for each sample
Supplementary files format and content: execel file includes raw miRNA count for each sample

source_name: Myocardium

extract_protocol:
RNA was isolated using miRNeasy Tissue/Cells Advanced Micro Kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries
Standard-specific mRNA sequencing (mRNA-seq) libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA). Standard miRNA libraries were generated using the NEXTFLEX small RNA-seq kit v3 (Perkin Elmer, Waltham, MA, USA)

value: Myocardium

tag: disease

value: DCM


title: S1_artificial_R_loop


title: HEK293 cells Ribo-seq [SM090F]

value: monosome footprints


title: 21s004530

description:
DCM_17_miRNA
named_count_matrix_miR.xlsx


title: MBN_artificial_R_loop


title: 21s004531

description:
DCM_18_miRNA
named_count_matrix_miR.xlsx


title: nosGAL4 WT #1

value: dissected 1-3 days post-eclosion

tag: developmental stage

value: Adult


title: nosGAL4 WT #2


title: 293FT cell, lactate, HA-IP, rep2

value: HA

value: HA-YAP


title: 21s004529

description:
DCM_14_miRNA
named_count_matrix_miR.xlsx


title: MBN_ssDRIP_seq_artificial_hybrid

data_processing:
Library strategy: DRIP-seq
For basic or modified ssDRIP-seq, reads were aligned to the genome with Bowtie 2 (version 2.3.4.2) using default settings. Duplicates were removed by Picard tools (http://broadinstitute.github.io/picard). Using samtools (version 1.3), unmapped reads and reads with more than three mismatches were removed, and the total mapped reads (non-strand R-loops) were divided into wR-loop and cR-loop reads (wR-loop means an R-loop with a Watson strand unpaired ssDNA, while cR-loop means an R-loop with a Crick strand unpaired ssDNA) . Aligned reads files (BAM) were converted to bigWig files by using deepTools (version 2.4.2).
Supplementary files format and content: bigWig

organism: Escherichia coli

source_name: plasmid

extract_protocol: To prepare RNA:DNA hybrid substrates, oligonucleotides of DNA (5'-ACGTGTCATGACTGACACTGGCAGTACGTAGCAGTGGTAGAACCTTCGTGTGCTTTCGCCAGCCCCAGACGGGTCAGATTTGGCAGATTGAGCGGGCCTTTACGACCGTTATCAGCTTCGCCTTTGGCACAAGCTTCTGCGATATGACCCAGGGTGTCAGCCCCGACGTCACCAAAGCGTTCTGCATCTTCTGTAGCGCCGATGCCGAATGAGTCCAGCACCATCCC

value: plasmid

tag: pulldown of

value: DNA:RNA hybrid

value: MBN digestion


title: 293FT cell, lactate, HA-IP, rep1


title: 21s004528

description:
ICM_13_miRNA
named_count_matrix_miR.xlsx

value: ICM


title: D3

city: Shenyang

first: JIE

last: LU

state: Liaoning

address: 77 Puhe Road, Shenbei Xiqu

department: Human Anatomy

institute: China Medical University

data_processing:
Bcl2fastq (v2.17.1.14) software was used for base-calling
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: Aug.2014(BDGP Release 6 + ISO1 MT/dm6)
Supplementary files format and content: FPKM values for each sample

source_name: Brain

extract_protocol:
The total RNA of each sample was extracted from the larvae brains by using TRIzol reagent (Life Technologies, USA)/RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s protocol. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double- stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA- tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor- ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: Brain


title: D2


title: 14DKO2, TCRseq

description:
10x Genomics
5‘RNA
PE150

data_processing:
Illumina Casava 1.8 software used for basecalling.
Single-cell RNA-seq data from each experiment were processed using a cell ranger count (10 × Genomics CellRanger [v3.1.0]), with reference to the mouse genome GRCm38 (mm10).
The digital gene expression matrices were analysed in R (v4.1.2) with the assistance of the Seurat (v4.0.0) package.
DoubletFinder software was used to identify and eliminate any potential doublets based on the proximity of each cell to artificial doublets. Cells exhibiting the expression of more than 10000 genes or fewer than 200 genes in UMI counts, along with those displaying over 10 % of mitochondrial gene expression, were excluded from the analysis. Subsequently, the filtered data underwent log normalisation and scaling to mitigate any cell-to-cell variations attributable to the UMI counts and percentage of mitochondrial reads.
Assembly: Mouse genome GRCm38 (mm10)
Supplementary files format and content: .tar: Tar archives include matrix table with raw gene counts for every gene and every cell (matrix.mtx), barcodes.tsv, and features.tsv.
Supplementary files format and content: .csv: Comma-separated text files with raw TCR counts for every clonetype and every cell.
Library strategy: TCR-seq

source_name: HCC

growth_protocol: Tumor infiltrating lymphocytes were isolated from tumor of mice hepatocellular carcinoma orthotopic transplantation model.

extract_protocol:
Single cell extracted from the mice bearing HCC were excised and mechanically dissociated into individual cells using a Tumour Dissociation Kit.
These individual cells were then collected using the 10 × Genomics Chromium Single Cell 5′ Solution. RNA-seq libraries were prepared according to the manufacturer’s protocol (10 × Genomics).

treatment_protocol: TILs isolated from mice hepatocellular carcinoma orthotopic transplantation model for the two groups (CON: control group, KO: KO group) at two time points (5Day and 14Day).

value: HCC

value: Tumor infiltrating cells

tag: time point


title: 21s004526

description:
ICM_7_miRNA
named_count_matrix_miR.xlsx


title: 14DKO1, TCRseq

description:
10x Genomics
5‘RNA
PE150


title: Selene (iPSC line#1)

description: 10x Genomics

value: iPSC-derived macrophages

value: WT


title: 293FT cell, lactate, input, rep1

value: HEK293FT cell

value: human embryonic kidney cell

value: clutured in glucose-free DMEM with exogenous 25mM lactate


title: C3

description: CON


title: 21s004525

description:
ICM_5_miRNA
named_count_matrix_miR.xlsx

value: Myocardium


title: C2

description: CON


title: 14DCON2, TCRseq

description:
10x Genomics
5‘RNA
PE150


title: D1


title: 21s004506

description:
DCM_19_mRNA
named_count_matrix.xlsx

value: DCM


title: 293FT cell, lactate, Flag-IP, rep1

value: Flag


title: 293FT cell, control, Flag-IP, rep1

value: cultured in glucose-free DMEM


title: C1

description: CON


title: 21s004505

description:
DCM_18_mRNA
named_count_matrix.xlsx


title: Female_PFC_BPA_RNA-seq rep3

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

data_processing:
Raw data were first analyzed by FastQC for quality control
Reads were trimmed with Trim Galore  (--quality 20 --phred33 --stringency 1 --length 20).
Clean data were aligned to the reference genome (UCSU, mm10) through HISAT2
SAMtools v1.6 were used to convert SAM files to BAM files, sort and build the alignment file index
FeatureCounts v1.6.3 from the Subread package was used for gene count with parameters set as: -t exon -g gene_id
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample.

source_name: prefrontal cortex

extract_protocol:
Prefrontal cortex were collected, flash frozen on dry ice, and RNA was harvested using RNeasy Lipid Tissue Mini Kit (Qiagen Cat. No. 74804). A total of 1 ug RNA was used for mRNA library preparation.
mRNA was captured by Oligo (dT) magnetic beads and the quality was evaluated on Agilent 2100 Bioanalyzer.

treatment_protocol: Timed-pregnant C57BL/6Slac mice were randomly assigned into two groups, receiving either corn oil (Ctrl) or BPA (40 ug/kg bw/day) administered by oral gavage from gestational day 0.5 to 13.5.

tag: strain

value: prefrontal cortex

tag: age

value: 4 months

tag: Sex

value: female

value: BPA (40 ug/kg bw/day)

tag: mouse id


title: 293FT cell, control, Flag-IP, rep2

tag: cell line

tag: cell type

tag: chip antibody

tag: treatment


title: 293FT cell, control, HA-IP, rep2

value: HA

value: HA-YAP


title: 21s004504

description:
DCM_17_mRNA
named_count_matrix.xlsx


title: 5DKO2, TCRseq

description:
10x Genomics
5‘RNA
PE150

value: HCC


title: 293FT cell, control, HA-IP, rep1


title: Female_PFC_BPA_RNA-seq rep2


title: 293FT cell, lactate, input, rep2


title: 21s004503

description:
DCM_14_mRNA
named_count_matrix.xlsx


title: 293FT cell, control, input, rep2


title: 5DCON2, TCRseq

description:
10x Genomics
5‘RNA
PE150

value: Tumor infiltrating cells


title: Female_PFC_BPA_RNA-seq rep1


title: 21s004501

description:
ICM_11_mRNA
named_count_matrix.xlsx

value: ICM


title: 293FT cell, control, input, rep1


title: 5DCON1, TCRseq

description:
10x Genomics
5‘RNA
PE150


title: Female_PFC_Ctrl_RNA-seq rep3

value: Corn oil


title: 21s004502

description:
ICM_13_mRNA
named_count_matrix.xlsx


title: 14DKO2, scRNAseq

description:
10x Genomics
5‘RNA
PE150

data_processing:
Illumina Casava 1.8 software used for basecalling.
Single-cell RNA-seq data from each experiment were processed using a cell ranger count (10 × Genomics CellRanger [v3.1.0]), with reference to the mouse genome GRCm38 (mm10).
The digital gene expression matrices were analysed in R (v4.1.2) with the assistance of the Seurat (v4.0.0) package.
DoubletFinder software was used to identify and eliminate any potential doublets based on the proximity of each cell to artificial doublets. Cells exhibiting the expression of more than 10000 genes or fewer than 200 genes in UMI counts, along with those displaying over 10 % of mitochondrial gene expression, were excluded from the analysis. Subsequently, the filtered data underwent log normalisation and scaling to mitigate any cell-to-cell variations attributable to the UMI counts and percentage of mitochondrial reads.
Assembly: Mouse genome GRCm38 (mm10)
Supplementary files format and content: .tar: Tar archives include matrix table with raw gene counts for every gene and every cell (matrix.mtx), barcodes.tsv, and features.tsv.
Supplementary files format and content: .csv: Comma-separated text files with raw TCR counts for every clonetype and every cell.


title: 14DCON1, TCRseq

description:
10x Genomics
5‘RNA
PE150


title: 21s004500

description:
ICM_7_mRNA
named_count_matrix.xlsx


title: HGC27 cell, lactate, rep2

data_processing:
Illumina Cassava1.7 software is used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence, the mapped to hg38 whole genome
RSEM (Version 1.3.3) was used for calculating the FPKM value.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Total RNA was extracted using Trizol following the standard protocol
Libraries were prepared according to Illumina's instructions

treatment_protocol: Cells were cultured in glucose-free DMEM with 10% FBS and 1% P.S. antibiotics and stimulated with lactate for 24h

value: human gastric cancer cell


title: Female_PFC_Ctrl_RNA-seq rep2


title: HGC27 cell, lactate, rep1

growth_protocol: Cells were cultured in glucose-free DMEM with 10% FBS and 1% P.S. antibiotics


title: Female_PFC_Ctrl_RNA-seq rep1


title: 14DKO1, scRNAseq

description:
10x Genomics
5‘RNA
PE150


title: Male_PFC_BPA_RNA-seq rep3

value: male


title: 21s004499

description:
ICM_5_mRNA
named_count_matrix.xlsx


title: Total Rnaseq CD201Low Adventicytes #3

city: Baltimore

first: Aaron

last: James

address: 720 Rutland Avenue, Ross Bldg., Room 529

institute: Johns Hopkins University

data_processing:
Single 75nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to Homo sapiens sequence GRCh38.p13 Dec-'19, with Partek Flow_99
FPKM calculation with Partek Flow as above
Supplementary files format and content: Tab-delimited .txt file, of Log2 quantile normalized FPKM

source_name: Adipose tissue

growth_protocol: Liposuction of healty donors was digested with collagenase type II (1mg/ml) for 50 min. After filtering, the stromal vascular fraction (SVF) was stained with antibodies to detect adventitial cells with the following immunophenotype: CD201High/Low CD34+CD31-CD45-.

extract_protocol:
CD201High or CD201Low CD34+CD45-CD31- cells were isolated by FACS and RNA immediately isolated with the GenElute™ Single Cell RNA Purification Kit (Sigma).
Standard Illumina stranded single-end protocols

treatment_protocol: Human lipoaspirate was digested with 1 mg/ml type II collagenase  in Dulbecco's Modified Eagle's Medium (DMEM) containing 0.5% bovine serum albumin at 37°C for 60 min under agitation, followed by centrifugation to remove adipocytes. The digested tissue was filtered using strainers (100 μm and 70 μm pore size) and washed with 2% fetal calf serum (FCS) in PBS (v/v). The cell pellet was resuspended and incubated in red cell lysis buffer (155 mM NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA) at RT for 10 min. After centrifugation, the stromal vascular fraction (SVF) was resuspended in PBS and filtered at 40 μm. Cells were then resuspended in 2% fetal calf serum (FCS) in PBS   and stained with the following antibodies: CD31, CD34, CD201 and CD45. Subsequently, adventitial cells (CD34+,CD146-,CD31-,CD45-) were sorted based on CD201 expression (CD201Low/High)

value: Adipose tissue

value: Freshly FACS sorted cells

tag: immunophenotype


title: 5DKO1,  TCRseq

description:
10x Genomics
5‘RNA
PE150


title: Male_PFC_BPA_RNA-seq rep2


title: 14DCON1, scRNAseq

description:
10x Genomics
5‘RNA
PE150


title: HGC27 cell, noglu, rep1

value: clutured in glucose-free DMEM


title: Total Rnaseq CD201Low Adventicytes #2


title: HGC27 cell, siAARS1, rep2

value: AARS1 knockdown

value: clutured in glucose-free DMEM with exogenous 25mM lactate


title: 5DKO2, scRNAseq

description:
10x Genomics
5‘RNA
PE150


title: Total Rnaseq CD201Low Adventicytes #1


title: Male_PFC_BPA_RNA-seq rep1

value: prefrontal cortex


title: 5DKO1, scRNAseq

description:
10x Genomics
5‘RNA
PE150


title: Male_PFC_Ctrl_RNA-seq rep3

value: 4 months


title: HGC27 cell, control, rep2

value: WT


title: Total RNAseq CD201High Adventicytes#3


title: Male_PFC_Ctrl_RNA-seq rep2


title: Total RNAseq CD201High Adventicytes#2


title: 5DCON2, scRNAseq

description:
10x Genomics
5‘RNA
PE150


title: HGC27 cell, siAARS1, rep1


title: 14DCON2, scRNAseq

description:
10x Genomics
5‘RNA
PE150


title: IgG_Cut&Run_LPKO_LCL_Rep1

status: Public on May 28 2024

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Aligned to hg38/EBV concatenated genome using Nextflow nf-core/cutandrun
Bam files were sorted (samtools) and converted to bedgraph files
Peaks were called using SEACR with IgG as background, and settings "norm" and "relaxed"
Bedgraph files were normalized by read depth and converted to bigwig files (bedGraphtoBigWig)
Assembly: hg38+NC007605
Supplementary files format and content: Bed files contain peaks called by SEACR using IgG as background control
Supplementary files format and content: Bigwig files contain normalized YY1 Cut&Run reads

source_name: LCL

extract_protocol:
Cut&Run was performed following kit protocol (Epicypher 14-1048) with a 1 min, 1% formaldehyde fixation
Libraries were prepared using the CUTANA CUT&RUN Library prep kit (Epicyhper 14-1001) according to protocol instructions with modifications. End repeat was modified to 20C for 20 minutes followed by 50C for 1 hour. PCR clean up beads (CNGS-0001) were used at 1.25x after ligation and 1.1x after indexing PCR to enrich for smaller fragments.

tag: donor

value: LCL

tag: cut&run antibody

value: IgG (Epicypher, 13-0042)

value: LPKO

value: IgG Control


title: Male_PFC_Ctrl_RNA-seq rep1

tag: tissue


title: HGC27 cell, noglu, rep2


title: YY1_Cut&Run_LPKO_LCL_Rep2

value: YY1 (CST, D5D9Z)

tag: genotype

value: YY1 Cut&Run


title: YY1_Cut&Run_LPKO_LCL_Rep1


title: YY1_Cut&Run_WT_LCL_Rep2


title: 5DCON1, scRNAseq

last: Xu

address: Huansha Roud

institute: Zhejiang University

description:
10x Genomics
5‘RNA
PE150

value: HCC

value: Tumor infiltrating cells


title: YY1_Cut&Run_WT_LCL_Rep1


title: ss_Cold_3h_Rep4

city: Frederiksberg

first: Swetha

last: Chenna

state: Choose State

address: Bülowsvej

country: Denmark

institute: University of Copenhagen

data_processing:
The reads were aligned using STAR v2.7.10a with parameters  --outSAMmultNmax 1, --alignEndsType Local, --clip3pAdapterSeq AGATCGGAAGAGC AGATCGGAAGAGC, --clip3pAdapterMMp 0.1 0.1
The reads that aligned below mapping quality of 10 were filtered out using samtools v1.6.
The duplicate reads are removed after fixing the mate pairs using samtools v1.6.
The strand specific coverage was calculated using bedtools (v2.30) genomecov
Assembly: EnsemblePlants v6.54
Supplementary files format and content: Normalised read counts in bedgraph format

organism: Manihot esculenta

source_name: Shoot

growth_protocol: Seedlings were grown in climate chambers with a long day photoperiod (16h light/8h dark cycle) at 20°C/18°C. Light intensity and humidity during control growth conditions was ~100 μE m−2 s−1 and 60% respectively.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with Turbo DNase (ThermoFisher Scientific) according to manufacturers’ instructions. DNase-treated RNA was recovered by acid–phenol extraction and ethanol precipitation.
Strand specific RNA-Seq libraries were prepared using TruSeq stranded total RNA preparation kit from Illumina following manufacturer's protocol.

treatment_protocol: For cold treatment, seedlings were grown in control conditions for two weeks and subsequently transferred to a cold room (4°C) with light for 3 h before harvesting.

tag: cultivar

value: Shoot

value: cold (4 C)

tag: time

value: 3 hours

tag: protocol

value: stranded RNA-Seq


title: HGC27 cell, control, rep1

value: human gastric cancer cell


title: ss_Cold_3h_Rep1


title: ss_Cold_3h_Rep2


title: Total RNAseq CD201High Adventicytes#1

value: Adipose tissue

value: Freshly FACS sorted cells


title: ss_WT_Rep4


title: ss_WT_Rep2


title: ss_Cold_3h_Rep3


title: H989

city: St. Louis

first: Antonina

middle: I.

last: Frolova

address: 660 S. Euclid Ave, CB 8064

department: OBGYN

institute: Washington University in St. Louis

data_processing:
Raw FASTQ files were used to perform analyses usingPartek®Flow®software, v10.0
RNA sequencing reads were aligned to the human mm39 primary assembly with STAR version 2.7.8a to generate BAM files.
Aligned reads were then quantified to the Ensembl transcript release 105 with STAR version 2.7.8a.
Gene counts were normalized with median ratio
Normalized counts were analyzed by DESeq2 to calculate differentially expressed genes (DEGs)
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw counts

source_name: Uterus

extract_protocol:
Total RNA was isolated using the RNeasy/QIAshredder Mini Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions
Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Uterus

value: Diet induced obesity


title: H941


title: ss_WT_Rep1

value: WT


title: ss_WT_Rep3


title: C965

value: Control


title: H811


title: H939


title: C972


title: H983


title: C979


title: h982


title: C919


title: Senescent cells under SIPS at day 12, Biological rep4

city: CDMX

first: Samael

last: Olascoaga

state: Iztapalapa

address: Av. San Rafael Atlixco

department: Health Sciences

country: Mexico

institute: Universidad Autonoma Metropolitana

description: Gene expression from senescent human prostate primary epithelial cells

hyb_protocol: We utilized 10 μl of total RNA (100 ng/μl) for amplification, labeling, and hybridization. This process was carried out using the Affymetrix Clariom Human D platform, adhering to the guidelines provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). The procedures occurred at the Instituto Nacional de Medicina Genómica (INMEGEN) in Mexico City.

data_processing: The CEL files obtained from INMEGEN were analyzed using the Transcriptome Analysis Console (TAC) software 4.0.2, employing the following parameters: Summarization method: SST-RMA, Gene-Level Use FDR: True, Limma – Anova Method: eBayes.

source_name: Normal human prostate epithelial cells (HPEC)

growth_protocol: These cells were grown on 100 mm Petri dishes using Prostate Epithelial Cell Basal Medium (ATCC® PCS-440-030™), without fetal bovine serum and phenol red. The medium was further enriched with the Prostate Epithelial Cell Growth Kit (ATCC® PCS-440-040™) and a 1% solution of streptomycin/penicillin from Gibco™ (Catalog number 15240062). We then kept the cells in an incubator at 37°C with a 5% CO2 atmosphere to ensure optimal growth conditions.

extract_protocol: Following the kit's guidelines, we extracted total RNA from 4 senescent and 4 control HPEC 100 mm Petri dishes that were 80% confluent using the RNeasy Mini Kit (Qiagen, catalog number 74104). The RNA's quantity was then measured with the Termofisher Nanodrop 2000 (Thermo Fisher Scientific, Wilmington, DE, USA) based on its provided protocol. Lastly, we evaluated the RNA's quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: We treated 2.8x10^6 HPEC cells to induce senescence with H2O2 (Sigma-Aldrich 30% (w/w) in H2O, catalog number: H1009-500ML). After seeding the cells, they were incubated with 12 μmol/L H2O2 in Prostate Epithelial Cell Basal Medium for 2 hours, 24 hours post-seeding. Once treated, we washed the cells twice with phosphate-buffered saline (PBS) and introduced a fresh medium. This medium was replaced every 48 hours. The senescence-induced HPEC cells were cultured in Prostate Epithelial Cell Basal Medium for another 12 days.

value: HPEC

tag: senescent

value: Yes


title: C915


title: C807


title: HD (HDVax treated CD4+ T cells from T3 TILs) FBC

first: Vladimir

last: Sukhov

address: 660. S Euclid Ave.

department: Immunology

data_processing:
10x Data was processed with the Cell Ranger pipeline, version 6.1.1. The downstream analysis was performed using the Seurat package.
Assembly: mm10
Supplementary files format and content: Comma separated files and matrix files

molecule: protein

source_name: Tumor

extract_protocol:
Live sorted cells were processed by the Genome Institute at Washington University
Library construction was generated using 10x libraries using 10X 5'v2 Single Cell RNAseq

value: Tumor

value: T3 Sarcoma

value: Tumor antigen specific CD4 T cells

value: WT mice

value: vaccines containing high doses (15 ug) of mItgb1 SLP


title: HD (HDVax treated CD4+ T cells from T3 TILs)


title: HD (HDVax treated CD4+ T cells from T3 TILs) TCR


title: C973


title: LD (LDVax treated CD4+ T cells from T3 TILs) FBC

value: vaccines containing low doses (1.5 ng) of mItgb1 SLP


title: LD (LDVax treated CD4+ T cells from T3 TILs) TCR


title: (CD4+ CD25- CD200-CD39+) 2

data_processing:
Data was processed by GTAC@MGI
The downstream analysis was performed using the R programming language.
Assembly: GRCm38.101
Supplementary files format and content: tab-separated values file includes raw counts for each sample

source_name: Tumor/spleen

extract_protocol:
Cells were lysed, and mRNA was extracted using Nucleospin RNA Plus (Cat#; 740990.50, TaKaRa)
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Tumor/spleen

tag: condition


title: PBS (PBS treated CD4+ T cells from T3 TILs)

value: PBS


title: (CD4+ CD25- CD200-CD39+) 3


title: (CD4+ CD25- CD200-CD39+) 1


title: PBS (PBS treated CD4+ T cells from T3 TILs) TCR


title: Senescent cells under SIPS at day 12, Biological rep3

scan_protocol: We utilized 10 μl of total RNA (100 ng/μl) for amplification, labeling, and hybridization. This process was carried out using the Affymetrix Clariom Human D platform, adhering to the guidelines provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). The procedures occurred at the Instituto Nacional de Medicina Genómica (INMEGEN) in Mexico City.


title: (CD4+ CD25- CD200+) 1

value: non Cluster-3/5


title: Proliferating cells, without H2O2, Biological rep3

description: Gene expression from normal human prostate primary epithelial cells in proliferation

label_protocol: We utilized 10 μl of total RNA (100 ng/μl) for amplification, labeling, and hybridization. This process was carried out using the Affymetrix Clariom Human D platform, adhering to the guidelines provided by the manufacturer (Affymetrix, Santa Clara, CA, USA). The procedures occurred at the Instituto Nacional de Medicina Genómica (INMEGEN) in Mexico City.

value: No


title: Senescent cells under SIPS at day 12, Biological rep2


title: (CD4+ CD25- CD200+) 2


title: (CD4+ CD25- CD200+) 3


title: Senescent cells under SIPS at day 12, Biological rep1


title: (CD4+ CD25+)Tregs 3


title: Proliferating cells, without H2O2, Biological rep4


title: LD (LDVax treated CD4+ T cells from T3 TILs)


title: Proliferating cells, without H2O2, Biological rep1


title: Proliferating cells, without H2O2, Biological rep2


title: (CD4+ CD25+)Tregs 1


title: Toyo, replicate 2, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-4.7). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: immune cell

value: Toyocamycin


title: DSS, mouse, repeat1, scRNA-seq

data_processing:
The CellRanger software pipeline(version 8.0.0) was used to align FASTQ sequencing reads to the mm10 reference transcriptome, and generating single cell feature counts for each sample.
Using Seruat version 4.0, each sample was considered for features shared by 3 or more cells, and cells showing 200 or more genes and less than 8000 genes. Cells with mitochondrial RNA percentages of >20 and nUMI > 20000 were filtered out.
Assembly: mm10
Supplementary files format and content: 10X Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Single-cell suspensions were loaded to 10X Chromium to capture 5000 single cells according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3).
Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol.

value: all cell


title: Toyo, replicate 3, RNA_seq


title: DSS, mouse, repeat2, scRNA-seq


title: PBS (PBS treated CD4+ T cells from T3 TILs) FBC


title: Toyo, replicate 1, RNA_seq


title: Ctrl, replicate 3, RNA_seq

value: Control


title: (CD4+ CD25+)Tregs 2


title: Ctrl, replicate 2, RNA_seq